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Smndc1 survival motor neuron domain containing 1 [ Rattus norvegicus (Norway rat) ]

Gene ID: 287768, updated on 28-Oct-2024

Summary

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Official Symbol
Smndc1provided by RGD
Official Full Name
survival motor neuron domain containing 1provided by RGD
Primary source
RGD:1309151
See related
EnsemblRapid:ENSRNOG00000014833 AllianceGenome:RGD:1309151
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Rattus norvegicus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary
Predicted to enable RNA binding activity. Predicted to be involved in RNA splicing; apoptotic process; and mRNA processing. Predicted to be located in Cajal body; cytoplasm; and nuclear speck. Predicted to be part of spliceosomal complex. Predicted to be active in nucleus. Orthologous to human SMNDC1 (survival motor neuron domain containing 1). [provided by Alliance of Genome Resources, Oct 2024]
Expression
Biased expression in Kidney (RPKM 116.0), Thymus (RPKM 115.6) and 9 other tissues See more
Orthologs
human mouse all
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Genomic context

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See Smndc1 in Genome Data Viewer
Location:
1q55
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (262395034..262406104, complement)
RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (252389675..252400749, complement)
106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (274096068..274107138, complement)

Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134484110 Neighboring gene uncharacterized LOC108349710 Neighboring gene MAX interactor 1, dimerization protein Neighboring gene uncharacterized LOC103691375 Neighboring gene U2 spliceosomal RNA Neighboring gene uncharacterized LOC102551352

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
  • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
  • BioProject: PRJNA238328
  • Publication: PMID 24510058
  • Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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Related articles in PubMed

  1. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Castello A, et al. Cell, 2012 Jun 8. PMID 22658674
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
  3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

GeneRIFs: Gene References Into Functions

Pathways from PubChem

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General gene information

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Markers

Homology

Clone Names

  • MGC112663

Gene Ontology Provided by RGD

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in apoptotic process IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Cajal body IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
survival of motor neuron-related-splicing factor 30
Names
survival motor neuron domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001025400.3 → NP_001020571.1  survival of motor neuron-related-splicing factor 30

    See identical proteins and their annotated locations for NP_001020571.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    BC097986, BC098697, CB726049, CV106705
    UniProtKB/Swiss-Prot
    Q4KM88, Q4QQU6
    UniProtKB/TrEMBL
    A0A8L2UPB2, A6JHV2
    Related
    ENSRNOP00000071875.3, ENSRNOT00000078670.3
    Conserved Domains (1) summary
    cd20399
    Location:73 → 128
    Tudor_SPF30; Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins

  2. NM_001035234.2 → NP_001030311.1  survival of motor neuron-related-splicing factor 30

    See identical proteins and their annotated locations for NP_001030311.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript. Variants 1 and 2 both encode the same protein.
    Source sequence(s)
    BC098697, CB726049, CV106705, EV778425
    UniProtKB/Swiss-Prot
    Q4KM88, Q4QQU6
    UniProtKB/TrEMBL
    A0A8L2UPB2, A6JHV2
    Conserved Domains (1) summary
    cd20399
    Location:73 → 128
    Tudor_SPF30; Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins

RNA

  1. NR_051995.1 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    BC098697, CB726049, CV106705, EV778425

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

  1. NC_086019.1 Reference GRCr8

    Range
    262395034..262406104 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_039102802.2 → XP_038958730.1  survival of motor neuron-related-splicing factor 30 isoform X1

    UniProtKB/Swiss-Prot
    Q4KM88, Q4QQU6
    UniProtKB/TrEMBL
    A0A8L2UPB2, A6JHV2
    Conserved Domains (1) summary
    cd20399
    Location:73 → 128
    Tudor_SPF30; Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins

  2. XM_063282691.1 → XP_063138761.1  survival of motor neuron-related-splicing factor 30 isoform X2

  3. XM_063282693.1 → XP_063138763.1  survival of motor neuron-related-splicing factor 30 isoform X2

  4. XM_063282694.1 → XP_063138764.1  survival of motor neuron-related-splicing factor 30 isoform X3

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q4QQU6.1 GenPept UniProtKB/Swiss-Prot:Q4QQU6

Gene LinkOut

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